The macro_pka_results Script
The macro_pka_results script can be used for a variety of post-processing actions on the results of a Macro-pKa calculation. The script assumes a set of protonated and deprotated tautomers and
conformers have been prepared in appropriately named files of
the form charge_*.mae, where the index refers to the total charge
relative to the input structure referenced in the input file.
The structures will be used as-is without further geometry optimization
or QM calculations. Post-processing takes a few seconds.
Process results at a different pH
You can calculate macro-pKa at a different pH, as well as see the breakdown of tautomer populations at the relevant charge transitions, by using the following command:
$SCHRODINGER/utilities/macro_pka_results -jobname <JOBNAME> -pH <X>
Process results with your own training data
To use a different set of training data to apply empirical corrections instead of the default, use the following command:
$SCHRODINGER/utilities/macro_pka_results -jobname <JOBNAME> -training_data <training.mae>
Process results with the Jaccard similarity method
To process the results using the Jaccard similarity method for empirical corrections , use the following command
$SCHRODINGER/utilities/macro_pka_results -jobname <JOBNAME> -use_jaccard